Evidence: native gel electrophoresis, Gel electrophoresis of the recombinant stem bromelain precursor protein displays a single band of around 38 kDa, which is in agreement with the predicted mass ...Evidence: native gel electrophoresis, Gel electrophoresis of the recombinant stem bromelain precursor protein displays a single band of around 38 kDa, which is in agreement with the predicted mass based on the single polypeptide chain of recombinant protein.
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
0 Å2
ΔGint
0 kcal/mol
Surface area
13080 Å2
Unit cell
Length a, b, c (Å)
64.310, 69.940, 74.250
Angle α, β, γ (deg.)
90.000, 90.000, 90.000
Int Tables number
18
Space group name H-M
P22121
-
Components
#1: Protein
FBSB
Mass: 36871.297 Da / Num. of mol.: 1 / Fragment: UNP Residues 25-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ananas comosus (pineapple) / Tissue: Stem / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O23799, UniProt: A0A199VSS3*PLUS
Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.26 Å3/Da / Density % sol: 45.68 % / Description: Clear thin plates
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: A reservoir solution comprised of 19% (w/v) PEG6000, 0.01 M Zinc chloride and 0.1 M MMT, pH4. Using an equal reservoir to protein (8 mg/ml) ratio, crystals were observed after 1 day and grew ...Details: A reservoir solution comprised of 19% (w/v) PEG6000, 0.01 M Zinc chloride and 0.1 M MMT, pH4. Using an equal reservoir to protein (8 mg/ml) ratio, crystals were observed after 1 day and grew to maximal size after 2 week. PH range: 3.8-4.2
-
Data collection
Diffraction
Mean temperature: 193 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953695 Å
Resolution: 3→47.38 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.778 / SU B: 23.855 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.564 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3138
323
4.6 %
RANDOM
Rwork
0.1982
-
-
-
obs
0.2032
6766
99.8 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi